[Biojava-l] EST assemblies

[Schreiber, Mark]

Hi -

With all of the recent discussion about alignments, I have been thinking
about ways to represent EST assemblies in biojava. Of course in reality
they are gapped alignments with potentially tens of thousands of
sequences. They also tend to carry some cruft around with them like a
consensus sequence (the alignment consensus) and the contig sequence -
basically the quality clipped and ungapped consensus. There needs to be
mapping between the contig sequence coordinates and the underlying
alignment coordinates. They also have interesting things like SNPs which
really only exist as columns in the alignment that exceed some threshold
conditions.

Some issues to think about:

1. How to best hold potentially thousands of sequences in an alignment.
One solution might be to store only the differences from the consensus
and infer the rest from the consensus.

2. How to represent the quality data, should the contig/ consensus
sequence be represented as PhredSequences, Sequences or maybe even
Markov Chains.

3. How to make a SNP like feature.

- Mark


Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

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